Gene Expression Omnibus (GEO) Overview

DataSet	:	Series(GSE) x Platform(GPL). A set of related gene expression data.
Sample	:	Biological materials.
platform	:	Methods or instruments used for the gene expression profilings.

All
(898,944)

SAGE NlaIII
(1,683)

SAGE RsaI
(3)

SAGE Sau3A
(54)

MPSS
(439)

GeneChip
(377,145)

Tiling Array
(21,846)

cDNA Array
(103,476)

Oligo Array
(239,584)

Other
(6,909)

adult aerial structure
(0)

young aerial structure
(0)

root
(0)

meristem/growing tissue
(0)

flower/sexual organ
(2)

seed/fruit/grain
(2)

pooled
(58)

unclassified
(606)

all
(6,909)

1 | 2 | 3 | 4 | 5 » [346]

	Sample ID	Title	Number of Data	Institute	Submission date	Platform	Sample type	Species	Organ class	Reasoning of the classification Keywords used for the classification are shown with bold font.
1	GSM231091	PIWI-associated piRNA in Drosophila melanogaster ovary (454 Pyrosequencing, 2006)	13,299	Yale University Stem Cell Center	2007-09-23	[Other] PIWI-associated piRNA in Drosophila melanogaster ovary (GPL5922)	other	Drosophila melanogaster	embryo	Lin laboratory, Yale University Stem Cell Center
2	GSM242040	HT3 delta PsbP	218	Washington University in Saint Louis	2007-11-09	[Other] Global proteomic characterization of photosystem II complexes from Synechocystis sp. PCC 6803 (GPL6115)	protein	Synechocystis sp. PCC 6803	unclassified	source_name:HT3 delta PsbP mutant HT3 wild type title:HT3 delta PsbP description:PSII Preparation: PSII was isolated from HT3, deltaPsbV HT3, deltaPsbQ HT3, and deltaPsbP HT3 strains as described previously . HT3 indicates the 6-His tagged CP47 used to affinity purify the complex . The final eluate from a Ni-NTA Agarose (Qiagen, Inc., Valencia, CA) column was suspended in 50 mM MES-NaOH pH 6.0, 10 mM CaCl2, 25% glycerol with 0.04% dodecyl maltoside. Chlorophyll concentrations were determined by methanol extraction and absorbance at 652 and 665 nm in a DW2000 spectrophotometer (SLM-Aminco, Urbana, IL) . AMT Peptide Identification: PSII preparations of approximately 1 mg protein were sent to Pacific Northwest National Laboratory (PNNL) for protein identification. The PSII samples were denatured by addition of equal volumes of 7 M urea, 2 M thiourea, and 1% CHAPS in 50 mM ammonium bicarbonate, pH 7.8 and then reduced with DTT to a final concentration of 5mM. CaCl2 was added to a final concentration of 1 mM. Samples were digested by the addition of sequencing grade modified trypsin (Promega, Madison, WI), using a ratio of 1:100 (wt/wt) protease to protein sample and incubated 4 hours at 37oC. Digests were desalted using Supelco Superclean SCX tubes (St. Louis, MO) with a Supelco vacuum manifold. The pH of each digestion was adjusted to 3.5 by addition of dilute formic acid. The SCX resin was conditioned with acetonitrile followed by 0.5 column volume (cv) 1M sodium formate. The column was washed with 2 cv of 25% acetonitrile in 500 mM ammonium acetate, pH 8.5 and the resin was re-equilibrated with 1 cv of 5% acetonitrile in 10 mM ammonium formate, pH 3.5. Peptide mixtures were loaded onto the resin and washed with 3 cv of 5% acetonitrile in 10 mM ammonium formate, pH 3.5. Peptides were eluted with 1 cv of 25% acetonitrile in 500 mM ammonium acetate, pH 8.5, followed by 0.5 cv of 100% acetonitrile. Eluted peptides were concentrated via Speedvac (ThermoSavant, San Jose, CA) to protein concentrations of 1.0 mg/mL, as determined by BCA assay (Pierce, Rockford, IL). Peptides were putatively identified using a capillary LC system, of a pair of model 100mL 100DM syringe pumps (Teledyne-Isco, Lincoln, NE), a series D controller (Teledyne-Isco, Lincoln, NE) and an in-house manufactured mixer, capillary column selector, and sample loop. Separations were achieved using a 5000 psi reversed-phase in-house packed capillary (150 um i.d., 360 um o.d., 60 cm long; Polymicro Technologies, Phoenix, AZ) by using an exponential gradient of 2 mobile-phase solvents consisting of 0.2% acetic acid and 0.05% trifluroacetic acid (TFA) in water and 0.1% TFA in 90% acetonitrile. Flow through the capillary HPLC column was ?1.8 uL/min when equilibrated to 100% mobile-phase 0.2% acetic acid and 0.05% TFA. For each HPLC sample, 10 ug was infused into a LCQ conventional ion trap MS (ThermoFinnigan, San Jose, CA) operating in a data dependent MS/MS mode over a 400 to 2000 m/Z range. For each cycle, the 3 most abundant ions from MC analysis were selected for MS/MS analysis by using a collision energy setting of 45%. Dynamic exclusion was used to discriminate against previously analyzed ions. The collision induced dissociation spectra from the conventional ion trap mass spectrophotometer were analyzed using SEQUEST and the genome sequence of Synechocystis 6803. PMT identifications were made based on a SEQUEST cross correlation (Xcorr) score ? 2.0, regardless of charge or mass. Using the same LC conditions, 5 ug of each sample analyzed in the ion trap was then analyzed in duplicate or triplicate by FTICR-MS. The FTICR mass spectrometers use ESI interfaced with an electrodynamic ion funnel assembly coupled to a radio frequency quadropole for collisional ion focusing and highly efficient ion accumulation and transport to a cylindrical FTICR for cell analysis . The resultant FTICR data was processed using the PRISM Data Analysis system, a series of software tools developed in-house. First the MS data was de-isotoped, giving the monoisotopic mass, charge, and intensity of the major peaks in each mass spectrum. Following this, the data was examined in a two-dimensional fashion to find groups of mass spectral peaks that were observed in sequential spectra. Each group, known as a unique mass class (UMC), has a median mass, central normalized elution time (NET), and abundance estimate, computed by summing the intensities of the MS peaks that compromise the UMC. The identity of each UMC was determined by comparing the mass and NET of each UMC with the mass and NETÃ¢â‚¬â„¢s of the 4423 PMTÃ¢â‚¬â„¢s in the Synechocystis 6803 AMT database (generated using the peptides observed from 23 LC/MS/MS). Search tolerances were Ã‚Â± 6 ppm for the mass and Ã‚Â±5% of the total run time for the elution time.
3	GSM242041	HT3 delta PsbQ	218	Washington University in Saint Louis	2007-11-09	[Other] Global proteomic characterization of photosystem II complexes from Synechocystis sp. PCC 6803 (GPL6115)	protein	Synechocystis sp. PCC 6803	unclassified	source_name:HT3 delta PsbQ HT3 wild type title:HT3 delta PsbQ description:PSII Preparation: PSII was isolated from HT3, deltaPsbV HT3, deltaPsbQ HT3, and deltaPsbP HT3 strains as described previously . HT3 indicates the 6-His tagged CP47 used to affinity purify the complex . The final eluate from a Ni-NTA Agarose (Qiagen, Inc., Valencia, CA) column was suspended in 50 mM MES-NaOH pH 6.0, 10 mM CaCl2, 25% glycerol with 0.04% dodecyl maltoside. Chlorophyll concentrations were determined by methanol extraction and absorbance at 652 and 665 nm in a DW2000 spectrophotometer (SLM-Aminco, Urbana, IL) . AMT Peptide Identification: PSII preparations of approximately 1 mg protein were sent to Pacific Northwest National Laboratory (PNNL) for protein identification. The PSII samples were denatured by addition of equal volumes of 7 M urea, 2 M thiourea, and 1% CHAPS in 50 mM ammonium bicarbonate, pH 7.8 and then reduced with DTT to a final concentration of 5mM. CaCl2 was added to a final concentration of 1 mM. Samples were digested by the addition of sequencing grade modified trypsin (Promega, Madison, WI), using a ratio of 1:100 (wt/wt) protease to protein sample and incubated 4 hours at 37oC. Digests were desalted using Supelco Superclean SCX tubes (St. Louis, MO) with a Supelco vacuum manifold. The pH of each digestion was adjusted to 3.5 by addition of dilute formic acid. The SCX resin was conditioned with acetonitrile followed by 0.5 column volume (cv) 1M sodium formate. The column was washed with 2 cv of 25% acetonitrile in 500 mM ammonium acetate, pH 8.5 and the resin was re-equilibrated with 1 cv of 5% acetonitrile in 10 mM ammonium formate, pH 3.5. Peptide mixtures were loaded onto the resin and washed with 3 cv of 5% acetonitrile in 10 mM ammonium formate, pH 3.5. Peptides were eluted with 1 cv of 25% acetonitrile in 500 mM ammonium acetate, pH 8.5, followed by 0.5 cv of 100% acetonitrile. Eluted peptides were concentrated via Speedvac (ThermoSavant, San Jose, CA) to protein concentrations of 1.0 mg/mL, as determined by BCA assay (Pierce, Rockford, IL). Peptides were putatively identified using a capillary LC system, of a pair of model 100mL 100DM syringe pumps (Teledyne-Isco, Lincoln, NE), a series D controller (Teledyne-Isco, Lincoln, NE) and an in-house manufactured mixer, capillary column selector, and sample loop. Separations were achieved using a 5000 psi reversed-phase in-house packed capillary (150 um i.d., 360 um o.d., 60 cm long; Polymicro Technologies, Phoenix, AZ) by using an exponential gradient of 2 mobile-phase solvents consisting of 0.2% acetic acid and 0.05% trifluroacetic acid (TFA) in water and 0.1% TFA in 90% acetonitrile. Flow through the capillary HPLC column was ?1.8 uL/min when equilibrated to 100% mobile-phase 0.2% acetic acid and 0.05% TFA. For each HPLC sample, 10 ug was infused into a LCQ conventional ion trap MS (ThermoFinnigan, San Jose, CA) operating in a data dependent MS/MS mode over a 400 to 2000 m/Z range. For each cycle, the 3 most abundant ions from MC analysis were selected for MS/MS analysis by using a collision energy setting of 45%. Dynamic exclusion was used to discriminate against previously analyzed ions. The collision induced dissociation spectra from the conventional ion trap mass spectrophotometer were analyzed using SEQUEST and the genome sequence of Synechocystis 6803. PMT identifications were made based on a SEQUEST cross correlation (Xcorr) score ? 2.0, regardless of charge or mass. Using the same LC conditions, 5 ug of each sample analyzed in the ion trap was then analyzed in duplicate or triplicate by FTICR-MS. The FTICR mass spectrometers use ESI interfaced with an electrodynamic ion funnel assembly coupled to a radio frequency quadropole for collisional ion focusing and highly efficient ion accumulation and transport to a cylindrical FTICR for cell analysis . The resultant FTICR data was processed using the PRISM Data Analysis system, a series of software tools developed in-house. First the MS data was de-isotoped, giving the monoisotopic mass, charge, and intensity of the major peaks in each mass spectrum. Following this, the data was examined in a two-dimensional fashion to find groups of mass spectral peaks that were observed in sequential spectra. Each group, known as a unique mass class (UMC), has a median mass, central normalized elution time (NET), and abundance estimate, computed by summing the intensities of the MS peaks that compromise the UMC. The identity of each UMC was determined by comparing the mass and NET of each UMC with the mass and NETÃ¢â‚¬â„¢s of the 4423 PMTÃ¢â‚¬â„¢s in the Synechocystis 6803 AMT database (generated using the peptides observed from 23 LC/MS/MS). Search tolerances were Ã‚Â± 6 ppm for the mass and Ã‚Â±5% of the total run time for the elution time.
4	GSM242042	HT3 delta PsbV	218	Washington University in Saint Louis	2007-11-09	[Other] Global proteomic characterization of photosystem II complexes from Synechocystis sp. PCC 6803 (GPL6115)	protein	Synechocystis sp. PCC 6803	unclassified	source_name:HT3 delta PsbV HT3 wild type title:HT3 delta PsbV description:PSII Preparation: PSII was isolated from HT3, deltaPsbV HT3, deltaPsbQ HT3, and deltaPsbP HT3 strains as described previously . HT3 indicates the 6-His tagged CP47 used to affinity purify the complex . The final eluate from a Ni-NTA Agarose (Qiagen, Inc., Valencia, CA) column was suspended in 50 mM MES-NaOH pH 6.0, 10 mM CaCl2, 25% glycerol with 0.04% dodecyl maltoside. Chlorophyll concentrations were determined by methanol extraction and absorbance at 652 and 665 nm in a DW2000 spectrophotometer (SLM-Aminco, Urbana, IL) . AMT Peptide Identification: PSII preparations of approximately 1 mg protein were sent to Pacific Northwest National Laboratory (PNNL) for protein identification. The PSII samples were denatured by addition of equal volumes of 7 M urea, 2 M thiourea, and 1% CHAPS in 50 mM ammonium bicarbonate, pH 7.8 and then reduced with DTT to a final concentration of 5mM. CaCl2 was added to a final concentration of 1 mM. Samples were digested by the addition of sequencing grade modified trypsin (Promega, Madison, WI), using a ratio of 1:100 (wt/wt) protease to protein sample and incubated 4 hours at 37oC. Digests were desalted using Supelco Superclean SCX tubes (St. Louis, MO) with a Supelco vacuum manifold. The pH of each digestion was adjusted to 3.5 by addition of dilute formic acid. The SCX resin was conditioned with acetonitrile followed by 0.5 column volume (cv) 1M sodium formate. The column was washed with 2 cv of 25% acetonitrile in 500 mM ammonium acetate, pH 8.5 and the resin was re-equilibrated with 1 cv of 5% acetonitrile in 10 mM ammonium formate, pH 3.5. Peptide mixtures were loaded onto the resin and washed with 3 cv of 5% acetonitrile in 10 mM ammonium formate, pH 3.5. Peptides were eluted with 1 cv of 25% acetonitrile in 500 mM ammonium acetate, pH 8.5, followed by 0.5 cv of 100% acetonitrile. Eluted peptides were concentrated via Speedvac (ThermoSavant, San Jose, CA) to protein concentrations of 1.0 mg/mL, as determined by BCA assay (Pierce, Rockford, IL). Peptides were putatively identified using a capillary LC system, of a pair of model 100mL 100DM syringe pumps (Teledyne-Isco, Lincoln, NE), a series D controller (Teledyne-Isco, Lincoln, NE) and an in-house manufactured mixer, capillary column selector, and sample loop. Separations were achieved using a 5000 psi reversed-phase in-house packed capillary (150 um i.d., 360 um o.d., 60 cm long; Polymicro Technologies, Phoenix, AZ) by using an exponential gradient of 2 mobile-phase solvents consisting of 0.2% acetic acid and 0.05% trifluroacetic acid (TFA) in water and 0.1% TFA in 90% acetonitrile. Flow through the capillary HPLC column was ?1.8 uL/min when equilibrated to 100% mobile-phase 0.2% acetic acid and 0.05% TFA. For each HPLC sample, 10 ug was infused into a LCQ conventional ion trap MS (ThermoFinnigan, San Jose, CA) operating in a data dependent MS/MS mode over a 400 to 2000 m/Z range. For each cycle, the 3 most abundant ions from MC analysis were selected for MS/MS analysis by using a collision energy setting of 45%. Dynamic exclusion was used to discriminate against previously analyzed ions. The collision induced dissociation spectra from the conventional ion trap mass spectrophotometer were analyzed using SEQUEST and the genome sequence of Synechocystis 6803. PMT identifications were made based on a SEQUEST cross correlation (Xcorr) score ? 2.0, regardless of charge or mass. Using the same LC conditions, 5 ug of each sample analyzed in the ion trap was then analyzed in duplicate or triplicate by FTICR-MS. The FTICR mass spectrometers use ESI interfaced with an electrodynamic ion funnel assembly coupled to a radio frequency quadropole for collisional ion focusing and highly efficient ion accumulation and transport to a cylindrical FTICR for cell analysis . The resultant FTICR data was processed using the PRISM Data Analysis system, a series of software tools developed in-house. First the MS data was de-isotoped, giving the monoisotopic mass, charge, and intensity of the major peaks in each mass spectrum. Following this, the data was examined in a two-dimensional fashion to find groups of mass spectral peaks that were observed in sequential spectra. Each group, known as a unique mass class (UMC), has a median mass, central normalized elution time (NET), and abundance estimate, computed by summing the intensities of the MS peaks that compromise the UMC. The identity of each UMC was determined by comparing the mass and NET of each UMC with the mass and NETÃ¢â‚¬â„¢s of the 4423 PMTÃ¢â‚¬â„¢s in the Synechocystis 6803 AMT database (generated using the peptides observed from 23 LC/MS/MS). Search tolerances were Ã‚Â± 6 ppm for the mass and Ã‚Â±5% of the total run time for the elution time.
5	GSM296634	ectopic p73 binding sites	4,224	Vanderbilt University Medical Center	2008-06-04	[Other] Human H1299 cells p73 ChIP-seq (GPL6931)	genomic	Homo sapiens	unclassified	source_name:H1299 cells, p73 IP sample title:ectopic p73 binding sites description:ChIPSeq experiment was contracted to GenPathway, Inc, San Diego, CA. Raw data files are not available.
6	GSM531766	Stage_II_Primordia	354,282	Utrecht University	2010-04-08	[Other] SAGE:16:DpnII:Schizophyllum commune (GPL10299)	SAGE	Schizophyllum commune	unclassified	source_name:Stage II Primordia title:Stage_II_Primordia description:Anchoring enzyme: DpnII
7	GSM531764	Monokaryon_vegetative_mycelium	318,644	Utrecht University	2010-04-08	[Other] SAGE:16:DpnII:Schizophyllum commune (GPL10299)	SAGE	Schizophyllum commune	pooled	Monokaryon, vegetative mycelium
8	GSM531765	Stage_I_Aggregates	293,178	Utrecht University	2010-04-08	[Other] SAGE:16:DpnII:Schizophyllum commune (GPL10299)	SAGE	Schizophyllum commune	unclassified	source_name:Stage I Aggregates title:Stage_I_Aggregates description:Anchoring enzyme: DpnII
9	GSM531767	Mature mushrooms	267,911	Utrecht University	2010-04-08	[Other] SAGE:16:DpnII:Schizophyllum commune (GPL10299)	SAGE	Schizophyllum commune	unclassified	source_name:Mushrooms title:Mature mushrooms description:Anchoring enzyme: DpnII
10	GSM71476	Rat1_Myc_serum_apoptosis_soluble	620	UTHSCSA	2005-08-22	[Other] Proteins in mitochondrial, chromatin, and soluble fractions of Myc-induced apoptosis in Rat1 fibroblasts (GPL2771)	protein	Rattus norvegicus	peripheral blood	Rat1_Myc_serum_apoptosis_soluble
11	GSM71477	Rat1_Myc_serum_apoptosis_chromatin	400	UTHSCSA	2005-08-22	[Other] Proteins in mitochondrial, chromatin, and soluble fractions of Myc-induced apoptosis in Rat1 fibroblasts (GPL2771)	protein	Rattus norvegicus	peripheral blood	Rat1_Myc_serum_apoptosis_chromatin
12	GSM71478	Rat1_Myc_serum_apoptosis_mitochondria	207	UTHSCSA	2005-08-22	[Other] Proteins in mitochondrial, chromatin, and soluble fractions of Myc-induced apoptosis in Rat1 fibroblasts (GPL2771)	protein	Rattus norvegicus	peripheral blood	Rat1_Myc_serum_apoptosis_mitochondria
13	GSM217365	Small RNAs from Dictyostelium discoideum: 5' dependent ligation	2,673	Uppsala University	2007-08-13	[Other] Dictyostelium discoideum small RNA sequences (GPL5734)	MPSS	Dictyostelium discoideum	unclassified	source_name:Dictyostelium discoideum title:Small RNAs from Dictyostelium discoideum: 5' dependent ligation description:cDNA library of small RNAs from Dictyostelium discoideum
14	GSM217366	Small RNAs from Dictyostelium discoideum: 5' independent ligation	2,673	Uppsala University	2007-08-13	[Other] Dictyostelium discoideum small RNA sequences (GPL5734)	MPSS	Dictyostelium discoideum	unclassified	source_name:Dictyostelium discoideum title:Small RNAs from Dictyostelium discoideum: 5' independent ligation description:cDNA library of small RNAs from Dictyostelium discoideum
15	GSM61947	Plasma membrane from Arabidopsis collected from two-phase partitioning (Sample 2)	304	University of Wisconsin	2005-06-21	[Other] 18O Isotopic Labeling of Plasma Membrane (GPL2543)	protein	Arabidopsis thaliana	unclassified	source_name:Plasma Membrane Microsomes (PM-depleted) title:Plasma membrane from Arabidopsis collected from two-phase partitioning (Sample 2) description:18O Isotopic labeling experiments conducted in order to identify proteins with PM localization.
16	GSM61946	Plasma membrane from Arabidopsis collected from two-phase partitioning (Sample 1)	236	University of Wisconsin	2005-06-21	[Other] 18O Isotopic Labeling of Plasma Membrane (GPL2543)	protein	Arabidopsis thaliana	unclassified	source_name:Plasma Membrane Microsomes (PM-depleted) title:Plasma membrane from Arabidopsis collected from two-phase partitioning (Sample 1) description:18O Isotopic labeling experiments conducted in order to identify proteins with PM localization.
17	GSM86382	Invitrogen yeast protoarray probed with YER125W WW domain 1, first experiment	12,288	University of Washington	2005-12-06	[Other] Invitrogen Yeast Protoarray (GPL3234)	protein	Saccharomyces cerevisiae	unclassified	source_name:E.coli overexpression strain title:Invitrogen yeast protoarray probed with YER125W WW domain 1, first experiment description:WW domain GST-fusion protein expressed and purified from E. coli, and chemically biotinylated with Pierce NHS-LC-LC-biotin
18	GSM86383	Invitrogen yeast protoarray probed with YER125W WW domain 1, second experiment	12,288	University of Washington	2005-12-06	[Other] Invitrogen Yeast Protoarray (GPL3234)	protein	Saccharomyces cerevisiae	unclassified	source_name:E.coli overexpression strain title:Invitrogen yeast protoarray probed with YER125W WW domain 1, second experiment description:WW domain GST-fusion protein expressed and purified from E. coli, and chemically biotinylated with Pierce NHS-LC-LC-biotin
19	GSM86384	Invitrogen yeast protoarray probed with YER125W WW domain 2, first experiment	12,288	University of Washington	2005-12-06	[Other] Invitrogen Yeast Protoarray (GPL3234)	protein	Saccharomyces cerevisiae	unclassified	source_name:E.coli overexpression strain title:Invitrogen yeast protoarray probed with YER125W WW domain 2, first experiment description:WW domain MBP-fusion protein expressed and purified from E. coli, and chemically biotinylated with Pierce NHS-LC-LC-biotin
20	GSM86385	Invitrogen yeast protoarray probed with YER125W WW domain 2, second experiment	12,288	University of Washington	2005-12-06	[Other] Invitrogen Yeast Protoarray (GPL3234)	protein	Saccharomyces cerevisiae	unclassified	source_name:E.coli overexpression strain title:Invitrogen yeast protoarray probed with YER125W WW domain 2, second experiment description:WW domain MBP-fusion protein expressed and purified from E. coli, and chemically biotinylated with Pierce NHS-LC-LC-biotin

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